Starting phenix.real_space_refine
on Wed Jul  1 22:32:50 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7wxg_32878/07_2026/7wxg_32878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wxg_32878/07_2026/7wxg_32878.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wxg_32878/07_2026/7wxg_32878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wxg_32878/07_2026/7wxg_32878.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7wxg_32878/07_2026/7wxg_32878.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7wxg_32878/07_2026/7wxg_32878.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wxg_32878/07_2026/7wxg_32878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wxg_32878/07_2026/7wxg_32878.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      15      5.16       5
     C    2048      2.51       5
     N     593      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3295
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3247
          Classifications: {'peptide': 430}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 414}
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'NAP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.76, per 1000 atoms: 0.23
  Number of scatterers: 3295
  At special positions: 0
  Unit cell: (80.56, 93.28, 60.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P       3     15.00
     O     636      8.00
     N     593      7.00
     C    2048      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 78.0 milliseconds
  

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  798

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 5 sheets defined
      49.5% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 348 through 364
    Processing helix  chain 'A' and resid 366 through 384
      removed outlier: 3.901A  pdb=" N   ARG A 370 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   SER A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 403
      removed outlier: 3.814A  pdb=" N   ILE A 388 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 413
    Processing helix  chain 'A' and resid 415 through 432
    Processing helix  chain 'A' and resid 471 through 484
      removed outlier: 4.333A  pdb=" N   GLN A 475 " --> pdb=" O   ASP A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 511
    Processing helix  chain 'A' and resid 524 through 534
      removed outlier: 3.672A  pdb=" N   ILE A 528 " --> pdb=" O   THR A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 579 through 592
    Processing helix  chain 'A' and resid 609 through 611
      No H-bonds generated for 'chain 'A' and resid 609 through 611'
    Processing helix  chain 'A' and resid 614 through 626
      removed outlier: 3.610A  pdb=" N   ASP A 618 " --> pdb=" O   ALA A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 640
    Processing helix  chain 'A' and resid 666 through 678
    Processing helix  chain 'A' and resid 689 through 700
    Processing helix  chain 'A' and resid 716 through 720
    Processing helix  chain 'A' and resid 740 through 742
      No H-bonds generated for 'chain 'A' and resid 740 through 742'
    Processing helix  chain 'A' and resid 757 through 761
      removed outlier: 3.557A  pdb=" N   PHE A 760 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444
      removed outlier: 7.232A  pdb=" N   VAL A 440 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   THR A 456 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ARG A 442 " --> pdb=" O   GLN A 454 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU A 751 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 749 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 486 through 488
      removed outlier: 6.258A  pdb=" N   LEU A 462 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   VAL A 461 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   ILE A 542 " --> pdb=" O   VAL A 461 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   LEU A 463 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ARG A 544 " --> pdb=" O   LEU A 463 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ILE A 465 " --> pdb=" O   ARG A 544 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 604 through 607
      removed outlier: 6.131A  pdb=" N   LEU A 604 " --> pdb=" O   GLU A 662 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   VAL A 664 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ILE A 606 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 683 through 685
      removed outlier: 6.862A  pdb=" N   ASP A 683 " --> pdb=" O   PHE A 706 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 728

    149 hydrogen bonds defined for protein.
    435 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.41

  Time building geometry restraints manager: 0.29 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.18 -     1.31: 571
        1.31 -     1.43: 791
        1.43 -     1.56: 1955
        1.56 -     1.68: 8
        1.68 -     1.81: 24
  Bond restraints: 3349
  Sorted by residual:
  bond pdb=" C1D NAP A 801 "
       pdb=" C2D NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.533  1.271  0.262 2.00e-02 2.50e+03 1.72e+02
  bond pdb=" C3D NAP A 801 "
       pdb=" C4D NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.518  1.261  0.257 2.00e-02 2.50e+03 1.65e+02
  bond pdb=" C3B NAP A 801 "
       pdb=" C4B NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.543  1.294  0.249 2.00e-02 2.50e+03 1.56e+02
  bond pdb=" C4B NAP A 801 "
       pdb=" O4B NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.426  1.623 -0.197 2.00e-02 2.50e+03 9.67e+01
  bond pdb=" C1D NAP A 801 "
       pdb=" O4D NAP A 801 "
    ideal  model  delta    sigma   weight residual
    1.375  1.550 -0.175 2.00e-02 2.50e+03 7.65e+01
  ... (remaining 3344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.97: 4500
        3.97 -     7.94: 33
        7.94 -    11.90: 5
       11.90 -    15.87: 3
       15.87 -    19.84: 3
  Bond angle restraints: 4544
  Sorted by residual:
  angle pdb=" N1A NAP A 801 "
        pdb=" C6A NAP A 801 "
        pdb=" N6A NAP A 801 "
      ideal   model   delta    sigma   weight residual
     119.30   99.46   19.84 3.00e+00 1.11e-01 4.37e+01
  angle pdb=" C1B NAP A 801 "
        pdb=" N9A NAP A 801 "
        pdb=" C4A NAP A 801 "
      ideal   model   delta    sigma   weight residual
     124.31  107.08   17.23 3.00e+00 1.11e-01 3.30e+01
  angle pdb=" C5A NAP A 801 "
        pdb=" C6A NAP A 801 "
        pdb=" N6A NAP A 801 "
      ideal   model   delta    sigma   weight residual
     122.73  139.91  -17.18 3.00e+00 1.11e-01 3.28e+01
  angle pdb=" C1B NAP A 801 "
        pdb=" N9A NAP A 801 "
        pdb=" C8A NAP A 801 "
      ideal   model   delta    sigma   weight residual
     129.84  145.62  -15.78 3.00e+00 1.11e-01 2.77e+01
  angle pdb=" O1N NAP A 801 "
        pdb=" PN  NAP A 801 "
        pdb=" O2N NAP A 801 "
      ideal   model   delta    sigma   weight residual
     122.51  109.58   12.93 3.00e+00 1.11e-01 1.86e+01
  ... (remaining 4539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.77: 1751
       14.77 -    29.54: 211
       29.54 -    44.30: 67
       44.30 -    59.07: 6
       59.07 -    73.84: 4
  Dihedral angle restraints: 2039
    sinusoidal: 807
      harmonic: 1232
  Sorted by residual:
  dihedral pdb=" CA  PHE A 642 "
           pdb=" C   PHE A 642 "
           pdb=" N   GLY A 643 "
           pdb=" CA  GLY A 643 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.98   21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  CYS A 598 "
           pdb=" C   CYS A 598 "
           pdb=" N   ASN A 599 "
           pdb=" CA  ASN A 599 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.95  -17.05     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  ALA A 714 "
           pdb=" C   ALA A 714 "
           pdb=" N   ASP A 715 "
           pdb=" CA  ASP A 715 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.01   15.99     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 2036 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 466
       0.072 -    0.144: 58
       0.144 -    0.215: 5
       0.215 -    0.287: 1
       0.287 -    0.359: 1
  Chirality restraints: 531
  Sorted by residual:
  chirality pdb=" C3D NAP A 801 "
            pdb=" C2D NAP A 801 "
            pdb=" C4D NAP A 801 "
            pdb=" O3D NAP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.38   -0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" C2B NAP A 801 "
            pdb=" C1B NAP A 801 "
            pdb=" C3B NAP A 801 "
            pdb=" O2B NAP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.50   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C2D NAP A 801 "
            pdb=" C1D NAP A 801 "
            pdb=" C3D NAP A 801 "
            pdb=" O2D NAP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.37   -0.18 2.00e-01 2.50e+01 8.07e-01
  ... (remaining 528 not shown)

  Planarity restraints: 588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 560 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO A 561 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 561 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 561 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 594 "    0.022 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A 595 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 595 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 595 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 469 "    0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO A 470 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 470 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 470 "    0.018 5.00e-02 4.00e+02
  ... (remaining 585 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 278
        2.73 -     3.27: 3683
        3.27 -     3.81: 5261
        3.81 -     4.36: 5991
        4.36 -     4.90: 10082
  Nonbonded interactions: 25295
  Sorted by model distance:
  nonbonded pdb=" O   SER A 410 "
            pdb=" OG  SER A 413 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   CYS A 570 "
            pdb=" ND1 HIS A 571 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" O   ASP A 530 "
            pdb=" OG  SER A 533 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   ALA A 399 "
            pdb=" OG  SER A 402 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" NH1 ARG A 525 "
            pdb=" O4B NAP A 801 "
     model   vdw
     2.272 3.120
  ... (remaining 25290 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.410
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.262   3349  Z= 0.580
  Angle     :  1.073  19.838   4544  Z= 0.492
  Chirality :  0.050   0.359    531
  Planarity :  0.004   0.033    588
  Dihedral  : 14.216  73.837   1241
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  7.54 %
    Favored  : 92.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.16 (0.29), residues: 428
  helix: -2.48 (0.29), residues: 186
  sheet: -4.14 (0.44), residues: 61
  loop : -4.14 (0.33), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 370 
 TYR   0.010   0.002   TYR A 573 
 PHE   0.021   0.002   PHE A 642 
 TRP   0.014   0.003   TRP A 768 
 HIS   0.003   0.001   HIS A 681 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01169 /  0.58 ( 3349)
  covalent geometry    : angle       1.07303 /  0.49 ( 4544)
  hydrogen bonds       : bond        0.14431 / 10.35 (  149)
  hydrogen bonds       : angle       6.36880 /  4.69 (  435)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 MET cc_start: 0.8692 (mtp) cc_final: 0.8466 (mtp)
REVERT: A  497 HIS cc_start: 0.8544 (m90) cc_final: 0.8323 (m90)
REVERT: A  521 LEU cc_start: 0.8997 (mt) cc_final: 0.8744 (mp)
REVERT: A  536 ASN cc_start: 0.8874 (t0) cc_final: 0.8492 (t0)
REVERT: A  594 TYR cc_start: 0.8507 (m-10) cc_final: 0.8192 (m-80)
REVERT: A  602 GLU cc_start: 0.8841 (pt0) cc_final: 0.8314 (mt-10)
REVERT: A  651 LYS cc_start: 0.9059 (mttt) cc_final: 0.8254 (tptt)
REVERT: A  652 HIS cc_start: 0.7686 (t-90) cc_final: 0.7389 (t-90)
REVERT: A  668 ASP cc_start: 0.7950 (t0) cc_final: 0.7629 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0598
  time to fit residues: 6.0611
Evaluate side-chains
  63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0670
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.9922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 375 ASN
A 392 ASN
A 434 HIS
A 536 ASN
A 607 HIS
A 672 ASN
A 681 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.120561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.096686 restraints weight = 6613.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.099867 restraints weight = 4222.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.102094 restraints weight = 3059.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.103867 restraints weight = 2430.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.105024 restraints weight = 2037.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3349  Z= 0.131
  Angle     :  0.645   6.273   4544  Z= 0.326
  Chirality :  0.045   0.162    531
  Planarity :  0.004   0.042    588
  Dihedral  :  6.417  44.149    480
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.22 %
    Favored  : 94.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.07 (0.36), residues: 428
  helix: -0.72 (0.35), residues: 191
  sheet: -3.46 (0.49), residues: 60
  loop : -2.95 (0.42), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 411 
 TYR   0.006   0.001   TYR A 631 
 PHE   0.013   0.002   PHE A 642 
 TRP   0.010   0.002   TRP A 748 
 HIS   0.004   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 3349)
  covalent geometry    : angle       0.64474 /  0.33 ( 4544)
  hydrogen bonds       : bond        0.03540 /  2.39 (  149)
  hydrogen bonds       : angle       4.92155 /  3.68 (  435)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 MET cc_start: 0.8949 (mtp) cc_final: 0.8715 (mtt)
REVERT: A  428 GLN cc_start: 0.8700 (mt0) cc_final: 0.8351 (tm-30)
REVERT: A  481 MET cc_start: 0.7782 (ttm) cc_final: 0.7528 (ptm)
REVERT: A  489 LEU cc_start: 0.9251 (mm) cc_final: 0.8982 (mm)
REVERT: A  497 HIS cc_start: 0.8318 (m90) cc_final: 0.8049 (t70)
REVERT: A  536 ASN cc_start: 0.8708 (t0) cc_final: 0.8259 (t0)
REVERT: A  556 GLN cc_start: 0.7991 (mt0) cc_final: 0.7698 (tt0)
REVERT: A  601 MET cc_start: 0.7867 (tmm) cc_final: 0.7644 (tmm)
REVERT: A  602 GLU cc_start: 0.8858 (pt0) cc_final: 0.8063 (mt-10)
REVERT: A  651 LYS cc_start: 0.8917 (mttt) cc_final: 0.8128 (tptt)
REVERT: A  652 HIS cc_start: 0.7693 (t-90) cc_final: 0.7349 (t-90)
REVERT: A  668 ASP cc_start: 0.7859 (t0) cc_final: 0.7544 (t0)
REVERT: A  712 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7675 (ttp-170)
  outliers start: 2
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0664
  time to fit residues: 7.0858
Evaluate side-chains
  62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 15 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 392 ASN
A 689 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.121769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.097501 restraints weight = 6401.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.100847 restraints weight = 4023.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.103293 restraints weight = 2887.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.105060 restraints weight = 2268.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.106330 restraints weight = 1892.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3349  Z= 0.112
  Angle     :  0.602   6.305   4544  Z= 0.305
  Chirality :  0.044   0.168    531
  Planarity :  0.004   0.046    588
  Dihedral  :  6.115  42.376    480
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.48 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.39), residues: 428
  helix: -0.02 (0.36), residues: 196
  sheet: -2.85 (0.53), residues: 63
  loop : -2.26 (0.47), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 384 
 TYR   0.005   0.001   TYR A 631 
 PHE   0.011   0.001   PHE A 642 
 TRP   0.008   0.002   TRP A 768 
 HIS   0.004   0.000   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 3349)
  covalent geometry    : angle       0.60245 /  0.31 ( 4544)
  hydrogen bonds       : bond        0.03313 /  2.20 (  149)
  hydrogen bonds       : angle       4.59949 /  3.46 (  435)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8616 (m-40) cc_final: 0.8300 (m110)
REVERT: A  473 LEU cc_start: 0.7956 (tt) cc_final: 0.7701 (tt)
REVERT: A  497 HIS cc_start: 0.8265 (m90) cc_final: 0.8024 (t70)
REVERT: A  536 ASN cc_start: 0.8617 (t0) cc_final: 0.8112 (t0)
REVERT: A  544 ARG cc_start: 0.6478 (tpt90) cc_final: 0.6233 (tpt90)
REVERT: A  556 GLN cc_start: 0.8035 (mt0) cc_final: 0.7755 (tt0)
REVERT: A  651 LYS cc_start: 0.8774 (mttt) cc_final: 0.7968 (tptt)
REVERT: A  668 ASP cc_start: 0.7875 (t0) cc_final: 0.7468 (t0)
REVERT: A  712 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7616 (ttp-170)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0652
  time to fit residues: 7.4739
Evaluate side-chains
  62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 392 ASN
A 695 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.121121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.096710 restraints weight = 6424.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.099986 restraints weight = 4130.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.102321 restraints weight = 2996.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.103874 restraints weight = 2369.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.105098 restraints weight = 2003.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3349  Z= 0.132
  Angle     :  0.631   8.989   4544  Z= 0.314
  Chirality :  0.044   0.171    531
  Planarity :  0.004   0.046    588
  Dihedral  :  6.077  38.386    480
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.40), residues: 428
  helix:  0.48 (0.37), residues: 197
  sheet: -2.58 (0.54), residues: 63
  loop : -2.01 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 551 
 TYR   0.011   0.001   TYR A 573 
 PHE   0.015   0.002   PHE A 696 
 TRP   0.009   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 3349)
  covalent geometry    : angle       0.63091 /  0.31 ( 4544)
  hydrogen bonds       : bond        0.03315 /  2.26 (  149)
  hydrogen bonds       : angle       4.52563 /  3.43 (  435)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7280 (tm-30)
REVERT: A  497 HIS cc_start: 0.8318 (m90) cc_final: 0.7942 (t70)
REVERT: A  536 ASN cc_start: 0.8619 (t0) cc_final: 0.8112 (t0)
REVERT: A  556 GLN cc_start: 0.7970 (mt0) cc_final: 0.7656 (tt0)
REVERT: A  565 HIS cc_start: 0.7334 (p-80) cc_final: 0.6706 (p90)
REVERT: A  602 GLU cc_start: 0.8907 (pt0) cc_final: 0.8153 (mt-10)
REVERT: A  651 LYS cc_start: 0.8714 (mttt) cc_final: 0.7950 (tptt)
REVERT: A  652 HIS cc_start: 0.7704 (t-90) cc_final: 0.7129 (t-90)
REVERT: A  668 ASP cc_start: 0.7868 (t0) cc_final: 0.7426 (t0)
REVERT: A  712 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7661 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0657
  time to fit residues: 6.8611
Evaluate side-chains
  58 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.124466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.099580 restraints weight = 6235.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.102918 restraints weight = 4004.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.105428 restraints weight = 2906.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.107088 restraints weight = 2290.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.108350 restraints weight = 1930.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3349  Z= 0.110
  Angle     :  0.608   8.574   4544  Z= 0.298
  Chirality :  0.043   0.157    531
  Planarity :  0.004   0.045    588
  Dihedral  :  5.970  36.058    480
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.41), residues: 428
  helix:  0.75 (0.38), residues: 196
  sheet: -2.43 (0.55), residues: 71
  loop : -1.77 (0.50), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 718 
 TYR   0.005   0.001   TYR A 631 
 PHE   0.010   0.002   PHE A 696 
 TRP   0.007   0.001   TRP A 768 
 HIS   0.003   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 3349)
  covalent geometry    : angle       0.60799 /  0.30 ( 4544)
  hydrogen bonds       : bond        0.03142 /  2.14 (  149)
  hydrogen bonds       : angle       4.30485 /  3.26 (  435)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 ASN cc_start: 0.8704 (m-40) cc_final: 0.8446 (m110)
REVERT: A  497 HIS cc_start: 0.8338 (m90) cc_final: 0.8092 (t70)
REVERT: A  503 MET cc_start: 0.8607 (mpp) cc_final: 0.7743 (mpp)
REVERT: A  536 ASN cc_start: 0.8583 (t0) cc_final: 0.8241 (t0)
REVERT: A  556 GLN cc_start: 0.7998 (mt0) cc_final: 0.7771 (tt0)
REVERT: A  565 HIS cc_start: 0.6996 (p-80) cc_final: 0.6494 (p-80)
REVERT: A  651 LYS cc_start: 0.8689 (mttt) cc_final: 0.8144 (ptpp)
REVERT: A  668 ASP cc_start: 0.7826 (t0) cc_final: 0.7419 (t0)
REVERT: A  712 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7617 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0576
  time to fit residues: 6.7753
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.124214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.099451 restraints weight = 6293.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.102855 restraints weight = 4049.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.105280 restraints weight = 2944.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.106975 restraints weight = 2332.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.108244 restraints weight = 1967.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3349  Z= 0.124
  Angle     :  0.633   7.517   4544  Z= 0.313
  Chirality :  0.044   0.154    531
  Planarity :  0.004   0.043    588
  Dihedral  :  5.966  35.551    480
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.41), residues: 428
  helix:  0.82 (0.38), residues: 196
  sheet: -2.21 (0.55), residues: 71
  loop : -1.78 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 718 
 TYR   0.008   0.001   TYR A 631 
 PHE   0.007   0.001   PHE A 616 
 TRP   0.008   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 ( 3349)
  covalent geometry    : angle       0.63326 /  0.31 ( 4544)
  hydrogen bonds       : bond        0.03192 /  2.16 (  149)
  hydrogen bonds       : angle       4.32318 /  3.25 (  435)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 GLN cc_start: 0.8015 (tt0) cc_final: 0.7458 (tm-30)
REVERT: A  497 HIS cc_start: 0.8328 (m90) cc_final: 0.8023 (m90)
REVERT: A  503 MET cc_start: 0.8008 (mpp) cc_final: 0.7590 (mpp)
REVERT: A  536 ASN cc_start: 0.8574 (t0) cc_final: 0.8087 (t0)
REVERT: A  555 GLN cc_start: 0.8883 (mp10) cc_final: 0.8604 (pp30)
REVERT: A  556 GLN cc_start: 0.7915 (mt0) cc_final: 0.7697 (tt0)
REVERT: A  565 HIS cc_start: 0.6974 (p-80) cc_final: 0.6453 (p90)
REVERT: A  629 LYS cc_start: 0.8312 (pptt) cc_final: 0.7985 (pptt)
REVERT: A  651 LYS cc_start: 0.8725 (mttt) cc_final: 0.8134 (ptpp)
REVERT: A  652 HIS cc_start: 0.7487 (t-90) cc_final: 0.7279 (t-90)
REVERT: A  668 ASP cc_start: 0.7797 (t0) cc_final: 0.7389 (t0)
REVERT: A  669 GLU cc_start: 0.7467 (tp30) cc_final: 0.7254 (tp30)
REVERT: A  712 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7599 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0634
  time to fit residues: 7.2912
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 3 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.124663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.099695 restraints weight = 6658.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.103046 restraints weight = 4303.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.105490 restraints weight = 3146.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.107220 restraints weight = 2502.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108363 restraints weight = 2113.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3349  Z= 0.166
  Angle     :  0.652   8.473   4544  Z= 0.327
  Chirality :  0.044   0.167    531
  Planarity :  0.004   0.043    588
  Dihedral  :  6.215  35.170    480
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.41), residues: 428
  helix:  0.90 (0.37), residues: 194
  sheet: -2.04 (0.56), residues: 69
  loop : -1.92 (0.47), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 411 
 TYR   0.004   0.001   TYR A 677 
 PHE   0.015   0.002   PHE A 387 
 TRP   0.012   0.002   TRP A 768 
 HIS   0.002   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.17 ( 3349)
  covalent geometry    : angle       0.65229 /  0.33 ( 4544)
  hydrogen bonds       : bond        0.03389 /  2.22 (  149)
  hydrogen bonds       : angle       4.46329 /  3.35 (  435)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 HIS cc_start: 0.8192 (m90) cc_final: 0.7938 (m90)
REVERT: A  503 MET cc_start: 0.7952 (mpp) cc_final: 0.7305 (mpp)
REVERT: A  536 ASN cc_start: 0.8627 (t0) cc_final: 0.8158 (t0)
REVERT: A  556 GLN cc_start: 0.7921 (mt0) cc_final: 0.7698 (tt0)
REVERT: A  602 GLU cc_start: 0.8895 (pt0) cc_final: 0.8549 (tt0)
REVERT: A  651 LYS cc_start: 0.8726 (mttt) cc_final: 0.8131 (ptpp)
REVERT: A  668 ASP cc_start: 0.7700 (t0) cc_final: 0.7326 (t0)
REVERT: A  712 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7903 (tpp80)
REVERT: A  724 GLU cc_start: 0.9122 (pp20) cc_final: 0.8855 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0594
  time to fit residues: 6.2165
Evaluate side-chains
  61 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0870
   chunk 5 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.3164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.125518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.100142 restraints weight = 6642.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.103616 restraints weight = 4190.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.106109 restraints weight = 3033.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.107883 restraints weight = 2402.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109143 restraints weight = 2022.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3349  Z= 0.143
  Angle     :  0.638   8.383   4544  Z= 0.320
  Chirality :  0.044   0.149    531
  Planarity :  0.004   0.043    588
  Dihedral  :  6.117  34.647    480
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.41), residues: 428
  helix:  0.98 (0.38), residues: 195
  sheet: -1.88 (0.56), residues: 70
  loop : -1.88 (0.48), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 411 
 TYR   0.006   0.001   TYR A 654 
 PHE   0.016   0.002   PHE A 387 
 TRP   0.009   0.002   TRP A 768 
 HIS   0.004   0.001   HIS A 565 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 3349)
  covalent geometry    : angle       0.63770 /  0.32 ( 4544)
  hydrogen bonds       : bond        0.03311 /  2.17 (  149)
  hydrogen bonds       : angle       4.42415 /  3.33 (  435)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  536 ASN cc_start: 0.8653 (t0) cc_final: 0.8155 (t0)
REVERT: A  556 GLN cc_start: 0.8014 (mt0) cc_final: 0.7774 (tt0)
REVERT: A  651 LYS cc_start: 0.8745 (mttt) cc_final: 0.8142 (ptpp)
REVERT: A  652 HIS cc_start: 0.7415 (t-90) cc_final: 0.7116 (t-90)
REVERT: A  668 ASP cc_start: 0.7721 (t0) cc_final: 0.7346 (t0)
REVERT: A  724 GLU cc_start: 0.9043 (pp20) cc_final: 0.8614 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0450
  time to fit residues: 4.7285
Evaluate side-chains
  59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 41 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.127158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.102872 restraints weight = 6483.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.106191 restraints weight = 4173.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.108437 restraints weight = 3045.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.110230 restraints weight = 2439.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.110838 restraints weight = 2058.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3349  Z= 0.124
  Angle     :  0.641   8.987   4544  Z= 0.320
  Chirality :  0.043   0.136    531
  Planarity :  0.004   0.045    588
  Dihedral  :  5.964  34.915    480
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.41), residues: 428
  helix:  1.01 (0.38), residues: 196
  sheet: -1.63 (0.58), residues: 70
  loop : -1.85 (0.48), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 718 
 TYR   0.003   0.001   TYR A 631 
 PHE   0.018   0.002   PHE A 387 
 TRP   0.008   0.002   TRP A 768 
 HIS   0.004   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 ( 3349)
  covalent geometry    : angle       0.64126 /  0.32 ( 4544)
  hydrogen bonds       : bond        0.03419 /  2.18 (  149)
  hydrogen bonds       : angle       4.38560 /  3.28 (  435)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  411 ARG cc_start: 0.8511 (ppt170) cc_final: 0.8188 (tmm-80)
REVERT: A  536 ASN cc_start: 0.8590 (t0) cc_final: 0.8079 (t0)
REVERT: A  555 GLN cc_start: 0.8774 (mp10) cc_final: 0.8442 (pp30)
REVERT: A  556 GLN cc_start: 0.8050 (mt0) cc_final: 0.7803 (tt0)
REVERT: A  651 LYS cc_start: 0.8737 (mttt) cc_final: 0.8171 (ptpp)
REVERT: A  668 ASP cc_start: 0.7679 (t0) cc_final: 0.7301 (t0)
REVERT: A  724 GLU cc_start: 0.9086 (pp20) cc_final: 0.8756 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0647
  time to fit residues: 6.6526
Evaluate side-chains
  64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.127386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.102481 restraints weight = 6528.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.105868 restraints weight = 4199.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.108308 restraints weight = 3071.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.109901 restraints weight = 2443.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.111222 restraints weight = 2079.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3349  Z= 0.123
  Angle     :  0.651   9.344   4544  Z= 0.323
  Chirality :  0.043   0.153    531
  Planarity :  0.004   0.045    588
  Dihedral  :  5.890  34.024    480
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.42), residues: 428
  helix:  1.15 (0.38), residues: 198
  sheet: -1.47 (0.60), residues: 69
  loop : -1.70 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 718 
 TYR   0.006   0.001   TYR A 654 
 PHE   0.019   0.002   PHE A 387 
 TRP   0.008   0.002   TRP A 768 
 HIS   0.003   0.000   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 3349)
  covalent geometry    : angle       0.65122 /  0.32 ( 4544)
  hydrogen bonds       : bond        0.03358 /  2.17 (  149)
  hydrogen bonds       : angle       4.28864 /  3.24 (  435)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  856 Ramachandran restraints generated.
    428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  411 ARG cc_start: 0.8430 (ppt170) cc_final: 0.8183 (tmm-80)
REVERT: A  521 LEU cc_start: 0.8144 (mm) cc_final: 0.7938 (mm)
REVERT: A  536 ASN cc_start: 0.8625 (t0) cc_final: 0.8115 (t0)
REVERT: A  555 GLN cc_start: 0.8765 (mp10) cc_final: 0.8434 (pp30)
REVERT: A  651 LYS cc_start: 0.8735 (mttt) cc_final: 0.8146 (ptpp)
REVERT: A  652 HIS cc_start: 0.7358 (t-90) cc_final: 0.7128 (t-90)
REVERT: A  668 ASP cc_start: 0.7704 (t0) cc_final: 0.7268 (t0)
REVERT: A  669 GLU cc_start: 0.7218 (tp30) cc_final: 0.7013 (tp30)
REVERT: A  724 GLU cc_start: 0.9107 (pp20) cc_final: 0.8730 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0522
  time to fit residues: 5.4214
Evaluate side-chains
  63 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0060
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.7196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 637 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.127168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.102310 restraints weight = 6565.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.105913 restraints weight = 3975.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.108554 restraints weight = 2801.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.110419 restraints weight = 2167.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.111757 restraints weight = 1799.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.4150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3349  Z= 0.120
  Angle     :  0.660   9.363   4544  Z= 0.328
  Chirality :  0.042   0.137    531
  Planarity :  0.004   0.046    588
  Dihedral  :  5.901  33.685    480
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.42), residues: 428
  helix:  1.24 (0.38), residues: 198
  sheet: -1.23 (0.62), residues: 69
  loop : -1.64 (0.49), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 718 
 TYR   0.004   0.001   TYR A 677 
 PHE   0.019   0.002   PHE A 387 
 TRP   0.009   0.002   TRP A 768 
 HIS   0.003   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 ( 3349)
  covalent geometry    : angle       0.66005 /  0.33 ( 4544)
  hydrogen bonds       : bond        0.03191 /  2.02 (  149)
  hydrogen bonds       : angle       4.22255 /  3.19 (  435)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 741.71 seconds
wall clock time: 13 minutes 28.92 seconds (808.92 seconds total)